PLINK not converting entire vcf to bed file
here is my code :
[ethan.kreuzer@hydra1 2_Population_stratification]$ plink --vcf ALL.2of4intersection.20100804.genotypes.vcf.gz --make-bed --out ALL.2of4intersection.20100804.genotypes
[mii] Please select a module to run plink:
MODULE PARENT(S)
1 plink/1.9b_6.21-x86_64 StdEnv/2020
2 plink/1.07 nixpkgs/16.09 intel/2018.3
3 plink/1.9b_5.2-x86_64 nixpkgs/16.09
4 plink/1.9b_4.1-x86_64 nixpkgs/16.09
Make a selection (1-4, q aborts) [1]: 1
[mii] loading StdEnv/2020 plink/1.9b_6.21-x86_64 ...
PLINK v1.90b6.21 64-bit (19 Oct 2020) www.cog-genomics.org/plink/1.9/
(C) 2005-2020 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to ALL.2of4intersection.20100804.genotypes.log.
Options in effect:
--make-bed
--out ALL.2of4intersection.20100804.genotypes
--vcf ALL.2of4intersection.20100804.genotypes.vcf.gz
50289 MB RAM detected; reserving 25144 MB for main workspace.
--vcf: 32k variants complete.
Error: File read failure.
[ethan.kreuzer@hydra1 2_Population_stratification]$ ls
1_Main_script_QC_GWAS.txt ALL.2of4intersection.20100804.genotypes-temporary.bed ALL.2of4intersection.20100804.genotypes.vcf.gz HapMap_3_r3_12.fam MDS_merged.R plink.fam
2_Main_script_MDS.txt ALL.2of4intersection.20100804.genotypes-temporary.bim HapMap_3_r3_12.bed HapMap_3_r3_12.log plink.bed plink.log
ALL.2of4intersection.20100804.genotypes.log ALL.2of4intersection.20100804.genotypes-temporary.fam HapMap_3_r3_12.bim indepSNP.prune.in plink.bim
Can someone help me understand how to convert the entire document vcf.gz file? Thank you
tutorial from : "https://github.com/MareesAT/GWA_tutorial/tree/master" in the "2_Population_stratification.zip" section
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Verify that your VCF file is readable all the way through and not corrupt/incomplete.
do you know how I could investigate this? I'm not sure what I should be looking for. Thank you for your reply.
I realize that it's not preinstalled on your system, but plink 2.0 provides a more useful error message here, and is generally a much better choice than plink 1.x for working with VCF data.